PD-vulnerable neurons are less resilient to cell stress induced by hydrogen peroxide

Figure 1-1

Nuclei (DAPI) count

Kurskal-Wallis


    Kruskal-Wallis rank sum test

data:  dapi_normalized by hydrogen_peroxide
Kruskal-Wallis chi-squared = 91.227, df = 3, p-value < 2.2e-16

Dunn test

  Comparison         Z      P.unadj        P.adj
1    0 - 100 3.4001879 6.733956e-04 4.040373e-03
2    0 - 150 7.8043915 5.978932e-15 3.587359e-14
3  100 - 150 3.9718484 7.131711e-05 4.279026e-04
4    0 - 200 8.1835348 2.756366e-16 1.653819e-15
5  100 - 200 4.5069337 6.577117e-06 3.946270e-05
6  150 - 200 0.7245953 4.687004e-01 1.000000e+00

Neuron count

Figure 2-1

Kurskal-Wallis


    Kruskal-Wallis rank sum test

data:  neuron_normalized by hydrogen_peroxide
Kruskal-Wallis chi-squared = 164.32, df = 3, p-value < 2.2e-16

Dunn test

  Comparison         Z      P.unadj        P.adj
1    0 - 100  5.867938 4.412478e-09 2.647487e-08
2    0 - 150  9.779527 1.378532e-22 8.271193e-22
3  100 - 150  3.408957 6.521186e-04 3.912712e-03
4    0 - 200 11.754230 6.717025e-32 4.030215e-31
5  100 - 200  5.563542 2.643538e-08 1.586123e-07
6  150 - 200  2.386850 1.699342e-02 1.019605e-01

Differential vulnerability of neurons to hydrogen peroxide

Figure 3-1

Kruskal-Wallis and Dunn test for each concetration

0 micromollar


    Kruskal-Wallis rank sum test

data:  neuron_normalized by neuron
Kruskal-Wallis chi-squared = 0.43515, df = 6, p-value = 0.9985
   Comparison           Z   P.unadj P.adj
1    DMV - LC  0.04600991 0.9633024     1
2     DMV - R -0.01706684 0.9863833     1
3      LC - R -0.05702708 0.9545236     1
4    DMV - SN  0.05968455 0.9524069     1
5     LC - SN  0.01204718 0.9903880     1
6      R - SN  0.06868787 0.9452381     1
7   DMV - STR  0.38805723 0.6979737     1
8    LC - STR  0.35874226 0.7197879     1
9     R - STR  0.34993891 0.7263845     1
10   SN - STR  0.36610036 0.7142902     1
11  DMV - VTA  0.39298245 0.6943324     1
12   LC - VTA  0.36444688 0.7155243     1
13    R - VTA  0.35739962 0.7207927     1
14   SN - VTA  0.37080616 0.7107819     1
15  STR - VTA  0.02239956 0.9821292     1
16  DMV - XII  0.34198331 0.7323635     1
17   LC - XII  0.30997827 0.7565775     1
18    R - XII  0.30876417 0.7575009     1
19   SN - XII  0.31538169 0.7524719     1
20  STR - XII -0.05916447 0.9528211     1
21  VTA - XII -0.07924845 0.9368350     1

100 micromollar


    Kruskal-Wallis rank sum test

data:  neuron_normalized by neuron
Kruskal-Wallis chi-squared = 27.496, df = 6, p-value = 0.0001169
   Comparison           Z      P.unadj        P.adj
1    DMV - LC  3.05767631 2.230604e-03 4.684268e-02
2     DMV - R  1.34734970 1.778676e-01 1.000000e+00
3      LC - R -0.98822521 3.230424e-01 1.000000e+00
4    DMV - SN  2.10964597 3.488886e-02 7.326661e-01
5     LC - SN -0.95978913 3.371614e-01 1.000000e+00
6      R - SN  0.28076187 7.788930e-01 1.000000e+00
7   DMV - STR -1.83772941 6.610229e-02 1.000000e+00
8    LC - STR -4.77623845 1.786046e-06 3.750697e-05
9     R - STR -2.81576290 4.866157e-03 1.021893e-01
10   SN - STR -3.87390539 1.071050e-04 2.249205e-03
11  DMV - VTA  1.13666428 2.556787e-01 1.000000e+00
12   LC - VTA -1.75714226 7.889356e-02 1.000000e+00
13    R - VTA -0.39951133 6.895165e-01 1.000000e+00
14   SN - VTA -0.86242974 3.884511e-01 1.000000e+00
15  STR - VTA  2.86680545 4.146378e-03 8.707394e-02
16  DMV - XII  1.29462100 1.954510e-01 1.000000e+00
17   LC - XII -1.93767522 5.266286e-02 1.000000e+00
18    R - XII -0.39459214 6.931439e-01 1.000000e+00
19   SN - XII -0.92310331 3.559534e-01 1.000000e+00
20  STR - XII  3.15425423 1.609088e-03 3.379086e-02
21  VTA - XII  0.03899101 9.688976e-01 1.000000e+00

150 micromollar


    Kruskal-Wallis rank sum test

data:  neuron_normalized by neuron
Kruskal-Wallis chi-squared = 43.006, df = 6, p-value = 1.163e-07
   Comparison           Z      P.unadj        P.adj
1    DMV - LC  3.40923177 6.514611e-04 1.368068e-02
2     DMV - R  1.86033898 6.283758e-02 1.000000e+00
3      LC - R -0.99814183 3.182106e-01 1.000000e+00
4    DMV - SN  4.59262928 4.376962e-06 9.191620e-05
5     LC - SN  1.12299366 2.614402e-01 1.000000e+00
6      R - SN  1.92817745 5.383306e-02 1.000000e+00
7   DMV - STR -0.91146407 3.620509e-01 1.000000e+00
8    LC - STR -3.86084771 1.129943e-04 2.372881e-03
9     R - STR -2.47917602 1.316863e-02 2.765412e-01
10   SN - STR -4.86157808 1.164536e-06 2.445526e-05
11  DMV - VTA  2.09242381 3.640062e-02 7.644130e-01
12   LC - VTA -1.07866488 2.807371e-01 1.000000e+00
13    R - VTA  0.02906247 9.768148e-01 1.000000e+00
14   SN - VTA -2.12809949 3.332884e-02 6.999055e-01
15  STR - VTA  2.71346613 6.658337e-03 1.398251e-01
16  DMV - XII  0.52063882 6.026184e-01 1.000000e+00
17   LC - XII -3.09940140 1.939121e-03 4.072154e-02
18    R - XII -1.50275652 1.329018e-01 1.000000e+00
19   SN - XII -4.36835989 1.251831e-05 2.628845e-04
20  STR - XII  1.39737195 1.623017e-01 1.000000e+00
21  VTA - XII -1.71656602 8.605850e-02 1.000000e+00

200 micromollar


    Kruskal-Wallis rank sum test

data:  neuron_normalized by neuron
Kruskal-Wallis chi-squared = 55.538, df = 6, p-value = 3.608e-10
   Comparison           Z      P.unadj        P.adj
1    DMV - LC  4.63069760 3.644358e-06 7.653152e-05
2     DMV - R  1.77727430 7.552312e-02 1.000000e+00
3      LC - R -1.77580383 7.576526e-02 1.000000e+00
4    DMV - SN  3.66003770 2.521781e-04 5.295741e-03
5     LC - SN -0.88166475 3.779581e-01 1.000000e+00
6      R - SN  1.09490499 2.735583e-01 1.000000e+00
7   DMV - STR -0.93784904 3.483220e-01 1.000000e+00
8    LC - STR -5.24022196 1.603836e-07 3.368055e-06
9     R - STR -2.47073125 1.348371e-02 2.831579e-01
10   SN - STR -4.34278531 1.406876e-05 2.954440e-04
11  DMV - VTA  0.27340288 7.845435e-01 1.000000e+00
12   LC - VTA -4.33119975 1.482991e-05 3.114281e-04
13    R - VTA -1.55404178 1.201745e-01 1.000000e+00
14   SN - VTA -3.37184576 7.466625e-04 1.567991e-02
15  STR - VTA  1.19097093 2.336650e-01 1.000000e+00
16  DMV - XII -0.06428897 9.487401e-01 1.000000e+00
17   LC - XII -5.00756106 5.512407e-07 1.157605e-05
18    R - XII -1.89119953 5.859771e-02 1.000000e+00
19   SN - XII -3.95024497 7.807125e-05 1.639496e-03
20  STR - XII  0.92177281 3.566471e-01 1.000000e+00
21  VTA - XII -0.35248092 7.244776e-01 1.000000e+00

Estimation statistics

0 micromollar

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:29 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  neuron_normalized

Unpaired mean difference of VTA (n = 20) minus SN (n = 30)
 0 [95CI  -0.179; 0.212]

Unpaired mean difference of LC (n = 24) minus SN (n = 30)
 0 [95CI  -0.168; 0.16]

Unpaired mean difference of R (n = 12) minus SN (n = 30)
 -1.11e-16 [95CI  -0.175; 0.16]

Unpaired mean difference of DMV (n = 19) minus SN (n = 30)
 0.00684 [95CI  -0.155; 0.16]

Unpaired mean difference of XII (n = 27) minus SN (n = 30)
 0 [95CI  -0.237; 0.238]

Unpaired mean difference of STR (n = 23) minus SN (n = 30)
 0.0303 [95CI  -0.174; 0.259]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

100 micromollar

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:29 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  neuron_normalized

Unpaired mean difference of VTA (n = 15) minus SN (n = 20)
 0.0605 [95CI  -0.142; 0.26]

Unpaired mean difference of LC (n = 24) minus SN (n = 20)
 -0.0838 [95CI  -0.213; 0.0524]

Unpaired mean difference of R (n = 8) minus SN (n = 20)
 0.0314 [95CI  -0.119; 0.187]

Unpaired mean difference of DMV (n = 16) minus SN (n = 20)
 0.197 [95CI  0.0662; 0.34]

Unpaired mean difference of XII (n = 23) minus SN (n = 20)
 0.152 [95CI  -0.0443; 0.388]

Unpaired mean difference of STR (n = 12) minus SN (n = 20)
 0.581 [95CI  0.35; 0.831]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

150 micromollar

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:29 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  neuron_normalized

Unpaired mean difference of VTA (n = 17) minus SN (n = 27)
 0.182 [95CI  -0.0308; 0.39]

Unpaired mean difference of LC (n = 24) minus SN (n = 27)
 0.0681 [95CI  -0.0918; 0.188]

Unpaired mean difference of R (n = 12) minus SN (n = 27)
 0.159 [95CI  -0.0317; 0.311]

Unpaired mean difference of DMV (n = 20) minus SN (n = 27)
 0.353 [95CI  0.192; 0.478]

Unpaired mean difference of XII (n = 26) minus SN (n = 27)
 0.388 [95CI  0.2; 0.595]

Unpaired mean difference of STR (n = 12) minus SN (n = 27)
 0.523 [95CI  0.308; 0.734]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

200 micromollar

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:29 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  neuron_normalized

Unpaired mean difference of VTA (n = 16) minus SN (n = 20)
 0.387 [95CI  0.139; 0.611]

Unpaired mean difference of LC (n = 24) minus SN (n = 20)
 -0.105 [95CI  -0.268; -0.0105]

Unpaired mean difference of R (n = 8) minus SN (n = 20)
 0.0239 [95CI  -0.151; 0.163]

Unpaired mean difference of DMV (n = 16) minus SN (n = 20)
 0.342 [95CI  0.146; 0.507]

Unpaired mean difference of XII (n = 20) minus SN (n = 20)
 0.365 [95CI  0.17; 0.534]

Unpaired mean difference of STR (n = 12) minus SN (n = 20)
 0.585 [95CI  0.322; 0.827]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

No overt difference in mitochondrial ROS production observed between neurons

Figure 4-1

Kruskal-Wallis


    Kruskal-Wallis rank sum test

data:  relative_oxidation by neuron
Kruskal-Wallis chi-squared = 133.58, df = 6, p-value < 2.2e-16

Dunn

   Comparison          Z      P.unadj        P.adj
1    DMV - LC -3.3231328 8.901252e-04 1.869263e-02
2     DMV - R -7.8362467 4.642135e-15 9.748483e-14
3      LC - R -2.3435415 1.910163e-02 4.011343e-01
4    DMV - SN -5.8719183 4.307810e-09 9.046400e-08
5     LC - SN -0.2064038 8.364755e-01 1.000000e+00
6      R - SN  2.8602152 4.233536e-03 8.890425e-02
7   DMV - STR -7.9501041 1.863548e-15 3.913451e-14
8    LC - STR -0.3988749 6.899854e-01 1.000000e+00
9     R - STR  2.9232967 3.463463e-03 7.273272e-02
10   SN - STR -0.2802927 7.792529e-01 1.000000e+00
11  DMV - VTA -5.1989318 2.004370e-07 4.209178e-06
12   LC - VTA  0.9733339 3.303874e-01 1.000000e+00
13    R - VTA  4.6926942 2.696303e-06 5.662237e-05
14   SN - VTA  1.8997528 5.746557e-02 1.000000e+00
15  STR - VTA  2.7090509 6.747598e-03 1.416996e-01
16  DMV - XII -7.9440379 1.957037e-15 4.109778e-14
17   LC - XII -0.5001405 6.169762e-01 1.000000e+00
18    R - XII  2.7666535 5.663492e-03 1.189333e-01
19   SN - XII -0.4371405 6.620094e-01 1.000000e+00
20  STR - XII -0.1955555 8.449581e-01 1.000000e+00
21  VTA - XII -2.8474318 4.407354e-03 9.255444e-02

Estimation statistics

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  relative_oxidation

Unpaired mean difference of VTA (n = 1338) minus SN (n = 576)
 -0.0276 [95CI  -0.0548; 0.000542]

Unpaired mean difference of LC (n = 181) minus SN (n = 576)
 -0.00436 [95CI  -0.0521; 0.0415]

Unpaired mean difference of R (n = 308) minus SN (n = 576)
 0.059 [95CI  0.018; 0.0987]

Unpaired mean difference of DMV (n = 2233) minus SN (n = 576)
 -0.0782 [95CI  -0.103; -0.0525]

Unpaired mean difference of XII (n = 1052) minus SN (n = 576)
 0.00677 [95CI  -0.0235; 0.0352]

Unpaired mean difference of STR (n = 1148) minus SN (n = 576)
 0.00515 [95CI  -0.0237; 0.0334]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

Comparing axonal vs std (note - very small effect - significant)

Welch Two Sample t-test - Axonal only


    Welch Two Sample t-test

data:  relative_oxidation by type
t = 4.0736, df = 3485, p-value = 4.732e-05
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 0.01993059 0.05691848
sample estimates:
mean in group non-vulnerable  mean in group pd-vulnerable 
                   0.5063470                    0.4679225 

Welch Two Sample t-test - STD only


    Welch Two Sample t-test

data:  relative_oxidation by type
t = 4.0736, df = 3485, p-value = 4.732e-05
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 0.01993059 0.05691848
sample estimates:
mean in group non-vulnerable  mean in group pd-vulnerable 
                   0.5063470                    0.4679225 

Comparing vulnerable vs non-vulnerable - significant by very small effect size

Welch Two Sample t-test


    Welch Two Sample t-test

data:  relative_oxidation by type
t = 6.016, df = 6820.1, p-value = 1.881e-09
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 0.02759581 0.05427272
sample estimates:
mean in group non-vulnerable  mean in group pd-vulnerable 
                   0.4884508                    0.4475166 

Intermitochondrial distance (roGFP)

Figure 4-2

Kurskal-Wallis


    Kruskal-Wallis rank sum test

data:  distance_um by neuron
Kruskal-Wallis chi-squared = 1.4927, df = 6, p-value = 0.96

Estimation statistics — not applicable

PD-vulnerable neurons have large axonal domains, that are globally more complex than PD-resilient neurons

Figure 6-1

Kruskal-Wallis


    Kruskal-Wallis rank sum test

data:  axon_area_per_neuron by neuron
Kruskal-Wallis chi-squared = 49.602, df = 6, p-value = 5.649e-09

Dunn

   Comparison          Z      P.unadj        P.adj
1    DMV - LC -1.4910572 1.359465e-01 1.000000e+00
2     DMV - R -2.1697753 3.002387e-02 6.305013e-01
3      LC - R -0.6949384 4.870939e-01 1.000000e+00
4    DMV - SN  0.3799178 7.040065e-01 1.000000e+00
5     LC - SN  1.7261794 8.431515e-02 1.000000e+00
6      R - SN  2.3506380 1.874126e-02 3.935664e-01
7   DMV - STR  1.8240271 6.814798e-02 1.000000e+00
8    LC - STR  2.9510478 3.166979e-03 6.650657e-02
9     R - STR  3.4823377 4.970564e-04 1.043819e-02
10   SN - STR  1.3978009 1.621729e-01 1.000000e+00
11  DMV - VTA  4.2860413 1.818852e-05 3.819588e-04
12   LC - VTA  5.3781860 7.524006e-08 1.580041e-06
13    R - VTA  5.8726242 4.289502e-09 9.007953e-08
14   SN - VTA  3.5891017 3.318193e-04 6.968206e-03
15  STR - VTA  1.7920665 7.312232e-02 1.000000e+00
16  DMV - XII  1.8995788 5.748842e-02 1.000000e+00
17   LC - XII  2.8822979 3.947864e-03 8.290513e-02
18    R - XII  3.3562827 7.899777e-04 1.658953e-02
19   SN - XII  1.5407671 1.233735e-01 1.000000e+00
20  STR - XII  0.3079467 7.581229e-01 1.000000e+00
21  VTA - XII -1.2158840 2.240291e-01 1.000000e+00

Estimation statistics

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  axon_area_per_neuron

Unpaired mean difference of VTA (n = 22) minus SN (n = 21)
 -9450 [95CI  -16900; -5080]

Unpaired mean difference of LC (n = 22) minus SN (n = 21)
 595 [95CI  -7340; 5640]

Unpaired mean difference of R (n = 19) minus SN (n = 21)
 2920 [95CI  -4570; 8600]

Unpaired mean difference of DMV (n = 30) minus SN (n = 21)
 -1290 [95CI  -8570; 4100]

Unpaired mean difference of XII (n = 9) minus SN (n = 21)
 -6940 [95CI  -15300; -1850]

Unpaired mean difference of STR (n = 14) minus SN (n = 21)
 -5660 [95CI  -13700; -190]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

PD-vulnerable vs PD-resilient


    Wilcoxon rank sum test with continuity correction

data:  data$axon_area_per_neuron by data$type
W = 723, p-value = 6.78e-10
alternative hypothesis: true location shift is not equal to 0
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
The first five rows are:
# A tibble: 5 × 9
  Count `Total Area` `Average Size` `%Area` neuron_number neuron
  <dbl>        <dbl>          <dbl>   <dbl>         <dbl> <fct> 
1  1652        63087           38.2   0.394             1 DMV   
2   814        53004           65.1   0.331             1 LC    
3  1094        46894           42.9   0.293             1 LC    
4  2062        77341           37.5   0.483             1 R     
5   820        25720           31.4   0.161             1 R     
# … with 3 more variables: axon_area_per_neuron <dbl>, count_per_neuron <dbl>,
#   type <fct>

X Variable :  type
Y Variable :  axon_area_per_neuron

Effect sizes(s) will be computed for:
  1. pd-vulnerable minus non-vulnerable
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  type
Y Variable :  axon_area_per_neuron

Unpaired mean difference of pd-vulnerable (n = 92) minus non-vulnerable (n = 45)
 8100 [95CI  5930; 10600]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

Kruskal-Wallis


    Kruskal-Wallis rank sum test

data:  count_per_neuron by neuron
Kruskal-Wallis chi-squared = 67.386, df = 6, p-value = 1.403e-12

Dunn

   Comparison          Z      P.unadj        P.adj
1    DMV - LC -2.1117441 3.470840e-02 7.288765e-01
2     DMV - R -4.9124144 8.996166e-07 1.889195e-05
3      LC - R -2.7062408 6.804969e-03 1.429043e-01
4    DMV - SN -2.8158643 4.864621e-03 1.021570e-01
5     LC - SN -0.6831796 4.944934e-01 1.000000e+00
6      R - SN  2.0185955 4.352928e-02 9.141149e-01
7   DMV - STR -2.4474832 1.438578e-02 3.021014e-01
8    LC - STR -0.5833195 5.596782e-01 1.000000e+00
9     R - STR  1.8401285 6.574937e-02 1.000000e+00
10   SN - STR  0.0260784 9.791948e-01 1.000000e+00
11  DMV - VTA  2.7269895 6.391507e-03 1.342216e-01
12   LC - VTA  4.5046159 6.649311e-06 1.396355e-04
13    R - VTA  7.0429233 1.882478e-12 3.953204e-11
14   SN - VTA  5.1351081 2.819820e-07 5.921621e-06
15  STR - VTA  4.5560173 5.213265e-06 1.094786e-04
16  DMV - XII  1.1254594 2.603944e-01 1.000000e+00
17   LC - XII  2.5790534 9.907147e-03 2.080501e-01
18    R - XII  4.6164416 3.903759e-06 8.197894e-05
19   SN - XII  3.0845492 2.038609e-03 4.281079e-02
20  STR - XII  2.8552967 4.299664e-03 9.029294e-02
21  VTA - XII -0.8534673 3.934002e-01 1.000000e+00

Estimation statistics

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  count_per_neuron

Unpaired mean difference of VTA (n = 22) minus SN (n = 21)
 -481 [95CI  -647; -330]

Unpaired mean difference of LC (n = 22) minus SN (n = 21)
 -147 [95CI  -329; 31]

Unpaired mean difference of R (n = 19) minus SN (n = 21)
 281 [95CI  73.5; 530]

Unpaired mean difference of DMV (n = 30) minus SN (n = 21)
 -254 [95CI  -443; -42.9]

Unpaired mean difference of XII (n = 9) minus SN (n = 21)
 -417 [95CI  -596; -260]

Unpaired mean difference of STR (n = 14) minus SN (n = 21)
 43.9 [95CI  -222; 375]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

PD-vulnerable vs PD-resilient


    Wilcoxon rank sum test with continuity correction

data:  data$count_per_neuron by data$type
W = 1068, p-value = 4.433e-06
alternative hypothesis: true location shift is not equal to 0
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
The first five rows are:
# A tibble: 5 × 9
  Count `Total Area` `Average Size` `%Area` neuron_number neuron
  <dbl>        <dbl>          <dbl>   <dbl>         <dbl> <fct> 
1  1652        63087           38.2   0.394             1 DMV   
2   814        53004           65.1   0.331             1 LC    
3  1094        46894           42.9   0.293             1 LC    
4  2062        77341           37.5   0.483             1 R     
5   820        25720           31.4   0.161             1 R     
# … with 3 more variables: axon_area_per_neuron <dbl>, count_per_neuron <dbl>,
#   type <fct>

X Variable :  type
Y Variable :  count_per_neuron

Effect sizes(s) will be computed for:
  1. pd-vulnerable minus non-vulnerable
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  type
Y Variable :  count_per_neuron

Unpaired mean difference of pd-vulnerable (n = 92) minus non-vulnerable (n = 45)
 245 [95CI  102; 368]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

Average segmentation length (µm)

Kruskal-Wallis


    Kruskal-Wallis rank sum test

data:  Average Size by neuron
Kruskal-Wallis chi-squared = 63.024, df = 6, p-value = 1.092e-11

Dunn

   Comparison           Z      P.unadj        P.adj
1    DMV - LC  1.03059727 3.027297e-01 1.000000e+00
2     DMV - R  3.60998615 3.062134e-04 6.430480e-03
3      LC - R  2.45591123 1.405279e-02 2.951085e-01
4    DMV - SN  6.35795802 2.044533e-10 4.293520e-09
5     LC - SN  4.98130378 6.315730e-07 1.326303e-05
6      R - SN  2.37043094 1.776736e-02 3.731146e-01
7   DMV - STR  5.32207495 1.025903e-07 2.154396e-06
8    LC - STR  4.19242298 2.759908e-05 5.795807e-04
9     R - STR  1.88561118 5.934737e-02 1.000000e+00
10   SN - STR -0.25035765 8.023108e-01 1.000000e+00
11  DMV - VTA  1.85882864 6.305143e-02 1.000000e+00
12   LC - VTA  0.77104145 4.406824e-01 1.000000e+00
13    R - VTA -1.71361442 8.659956e-02 1.000000e+00
14   SN - VTA -4.21928067 2.450830e-05 5.146743e-04
15  STR - VTA -3.51242834 4.440317e-04 9.324666e-03
16  DMV - XII  0.81906785 4.127477e-01 1.000000e+00
17   LC - XII  0.05563405 9.556333e-01 1.000000e+00
18    R - XII -1.84639479 6.483490e-02 1.000000e+00
19   SN - XII -3.75914928 1.704921e-04 3.580334e-03
20  STR - XII -3.30324274 9.557362e-04 2.007046e-02
21  VTA - XII -0.53190012 5.947952e-01 1.000000e+00

Estimation statistics

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  Average Size

Unpaired mean difference of VTA (n = 22) minus SN (n = 21)
 64.6 [95CI  31.4; 99.1]

Unpaired mean difference of LC (n = 22) minus SN (n = 21)
 35.8 [95CI  15.4; 52.3]

Unpaired mean difference of R (n = 19) minus SN (n = 21)
 7.73 [95CI  -13.3; 18.4]

Unpaired mean difference of DMV (n = 30) minus SN (n = 21)
 77.3 [95CI  50.9; 104]

Unpaired mean difference of XII (n = 9) minus SN (n = 21)
 39.6 [95CI  13.6; 59.7]

Unpaired mean difference of STR (n = 14) minus SN (n = 21)
 -5.7 [95CI  -27; 5.07]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

PD-vulnerable vs PD-resilient


    Wilcoxon rank sum test with continuity correction

data:  data$`Average Size` by data$type
W = 1887, p-value = 0.4029
alternative hypothesis: true location shift is not equal to 0
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
The first five rows are:
# A tibble: 5 × 9
  Count `Total Area` `Average Size` `%Area` neuron_number neuron
  <dbl>        <dbl>          <dbl>   <dbl>         <dbl> <fct> 
1  1652        63087           38.2   0.394             1 DMV   
2   814        53004           65.1   0.331             1 LC    
3  1094        46894           42.9   0.293             1 LC    
4  2062        77341           37.5   0.483             1 R     
5   820        25720           31.4   0.161             1 R     
# … with 3 more variables: axon_area_per_neuron <dbl>, count_per_neuron <dbl>,
#   type <fct>

X Variable :  type
Y Variable :  Average Size

Effect sizes(s) will be computed for:
  1. pd-vulnerable minus non-vulnerable
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  type
Y Variable :  Average Size

Unpaired mean difference of pd-vulnerable (n = 92) minus non-vulnerable (n = 45)
 -2.4 [95CI  -23; 17.6]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

PD-vulnerable neurons have a higher proportion of varicosities that are positive for Syt1

Figure 7-1

Kruskal-Wallis


    Kruskal-Wallis rank sum test

data:  percentage_syt1_positive by neuron
Kruskal-Wallis chi-squared = 59.589, df = 6, p-value = 5.456e-11

Dunn

   Comparison          Z      P.unadj        P.adj
1    DMV - LC  0.8368274 4.026896e-01 1.000000e+00
2     DMV - R -1.5062893 1.319929e-01 1.000000e+00
3      LC - R -2.3431167 1.912340e-02 4.015914e-01
4    DMV - SN -0.1422607 8.868741e-01 1.000000e+00
5     LC - SN -0.9790881 3.275365e-01 1.000000e+00
6      R - SN  1.3640287 1.725585e-01 1.000000e+00
7   DMV - STR  3.0042104 2.662711e-03 5.591694e-02
8    LC - STR  2.1673830 3.020566e-02 6.343189e-01
9     R - STR  4.5104997 6.467508e-06 1.358177e-04
10   SN - STR  3.1464711 1.652536e-03 3.470326e-02
11  DMV - VTA  3.1632076 1.560410e-03 3.276861e-02
12   LC - VTA  2.3263802 1.999828e-02 4.199638e-01
13    R - VTA  4.6694969 3.019382e-06 6.340702e-05
14   SN - VTA  3.3054683 9.481784e-04 1.991175e-02
15  STR - VTA  0.1589972 8.736711e-01 1.000000e+00
16  DMV - XII  4.7197066 2.361851e-06 4.959887e-05
17   LC - XII  3.8828792 1.032269e-04 2.167764e-03
18    R - XII  6.2259959 4.785065e-10 1.004864e-08
19   SN - XII  4.8619672 1.162249e-06 2.440722e-05
20  STR - XII  1.7154962 8.625429e-02 1.000000e+00
21  VTA - XII  1.5564990 1.195895e-01 1.000000e+00

Estimation statistics

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  percentage_syt1_positive

Unpaired mean difference of VTA (n = 12) minus SN (n = 12)
 -32.1 [95CI  -43.2; -19.3]

Unpaired mean difference of LC (n = 12) minus SN (n = 12)
 -8.15 [95CI  -18; 2.03]

Unpaired mean difference of R (n = 12) minus SN (n = 12)
 11.3 [95CI  1.79; 20.9]

Unpaired mean difference of DMV (n = 12) minus SN (n = 12)
 -1.49 [95CI  -10.9; 7.75]

Unpaired mean difference of XII (n = 12) minus SN (n = 12)
 -48.1 [95CI  -56.9; -38.5]

Unpaired mean difference of STR (n = 12) minus SN (n = 12)
 -30 [95CI  -40.4; -17.5]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

PD-vulnerable vs PD-resilient


    Wilcoxon rank sum exact test

data:  data_percentage_syt1_positive$percentage_syt1_positive by data_percentage_syt1_positive$type
W = 79, p-value = 2.941e-16
alternative hypothesis: true location shift is not equal to 0
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
The first five rows are:
# A tibble: 5 × 6
  neuron image negative positive percentage_syt1_positive type         
  <fct>  <chr>    <int>    <int>                    <dbl> <fct>        
1 SN     SN_01      358      439                     55.1 pd-vulnerable
2 SN     SN_02      244      128                     34.4 pd-vulnerable
3 SN     SN_03      361      492                     57.7 pd-vulnerable
4 SN     SN_04      286      210                     42.3 pd-vulnerable
5 SN     SN_05      141      488                     77.6 pd-vulnerable

X Variable :  type
Y Variable :  percentage_syt1_positive

Effect sizes(s) will be computed for:
  1. pd-vulnerable minus non-vulnerable
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  type
Y Variable :  percentage_syt1_positive

Unpaired mean difference of pd-vulnerable (n = 48) minus non-vulnerable (n = 36)
 37.1 [95CI  30.7; 43]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

Kruskal-Wallis


    Kruskal-Wallis rank sum test

data:  mean_nearest_varicsotiey by neuron
Kruskal-Wallis chi-squared = 28.368, df = 6, p-value = 8.011e-05

Dunn

   Comparison          Z      P.unadj        P.adj
1    DMV - LC  0.8703005 3.841362e-01 1.0000000000
2     DMV - R -0.5941475 5.524135e-01 1.0000000000
3      LC - R -1.4644480 1.430716e-01 1.0000000000
4    DMV - SN  3.1297345 1.749644e-03 0.0367425146
5     LC - SN  2.2594340 2.385640e-02 0.5009844259
6      R - SN  3.7238820 1.961827e-04 0.0041198361
7   DMV - STR  1.5732355 1.156643e-01 1.0000000000
8    LC - STR  0.7029350 4.820962e-01 1.0000000000
9     R - STR  2.1673830 3.020566e-02 0.6343189291
10   SN - STR -1.5564990 1.195895e-01 1.0000000000
11  DMV - VTA  2.0334906 4.200298e-02 0.8820626214
12   LC - VTA  1.1631901 2.447524e-01 1.0000000000
13    R - VTA  2.6276381 8.597994e-03 0.1805578807
14   SN - VTA -1.0962439 2.729721e-01 1.0000000000
15  STR - VTA  0.4602551 6.453331e-01 1.0000000000
16  DMV - XII -1.2133997 2.249770e-01 1.0000000000
17   LC - XII -2.0837002 3.718744e-02 0.7809362753
18    R - XII -0.6192523 5.357502e-01 1.0000000000
19   SN - XII -4.3431343 1.404642e-05 0.0002949749
20  STR - XII -2.7866353 5.325838e-03 0.1118426079
21  VTA - XII -3.2468903 1.166733e-03 0.0245013998

Estimation Statistics

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  mean_nearest_varicsotiey

Unpaired mean difference of VTA (n = 12) minus SN (n = 12)
 0.162 [95CI  -0.0767; 0.415]

Unpaired mean difference of LC (n = 12) minus SN (n = 12)
 0.406 [95CI  0.183; 0.789]

Unpaired mean difference of R (n = 12) minus SN (n = 12)
 0.871 [95CI  0.507; 1.5]

Unpaired mean difference of DMV (n = 12) minus SN (n = 12)
 0.74 [95CI  0.375; 1.41]

Unpaired mean difference of XII (n = 12) minus SN (n = 12)
 1.33 [95CI  0.708; 3.44]

Unpaired mean difference of STR (n = 12) minus SN (n = 12)
 0.331 [95CI  0.0556; 0.717]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

PD-vulnerable vs PD-resilient


    Wilcoxon rank sum exact test

data:  mean_varicosity_nn_length$mean_nearest_varicsotiey by mean_varicosity_nn_length$type
W = 875, p-value = 0.9248
alternative hypothesis: true location shift is not equal to 0
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
The first five rows are:
# A tibble: 5 × 5
  neuron image mean_nearest_varicsotiey     n type         
  <fct>  <chr>                    <dbl> <int> <fct>        
1 SN     SN_01                     2.74   797 pd-vulnerable
2 SN     SN_02                     2.72   372 pd-vulnerable
3 SN     SN_03                     2.90   853 pd-vulnerable
4 SN     SN_04                     2.89   496 pd-vulnerable
5 SN     SN_05                     2.99   629 pd-vulnerable

X Variable :  type
Y Variable :  mean_nearest_varicsotiey

Effect sizes(s) will be computed for:
  1. pd-vulnerable minus non-vulnerable
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  type
Y Variable :  mean_nearest_varicsotiey

Unpaired mean difference of pd-vulnerable (n = 48) minus non-vulnerable (n = 36)
 -0.104 [95CI  -0.725; 0.242]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

Kruskal-Wallis


    Kruskal-Wallis rank sum test

data:  mean_axon_per_var_px by neuron
Kruskal-Wallis chi-squared = 62.576, df = 6, p-value = 1.346e-11

Dunn

   Comparison          Z      P.unadj        P.adj
1    DMV - LC  4.6611287 3.144800e-06 6.604081e-05
2     DMV - R  4.1506639 3.315122e-05 6.961756e-04
3      LC - R -0.5104647 6.097259e-01 1.000000e+00
4    DMV - SN  4.4519218 8.510516e-06 1.787208e-04
5     LC - SN -0.2092069 8.342868e-01 1.000000e+00
6      R - SN  0.3012579 7.632179e-01 1.000000e+00
7   DMV - STR  6.1255766 9.035577e-10 1.897471e-08
8    LC - STR  1.4644480 1.430716e-01 1.000000e+00
9     R - STR  1.9749127 4.827806e-02 1.000000e+00
10   SN - STR  1.6736548 9.419846e-02 1.000000e+00
11  DMV - VTA  2.5857967 9.715422e-03 2.040239e-01
12   LC - VTA -2.0753320 3.795578e-02 7.970713e-01
13    R - VTA -1.5648673 1.176140e-01 1.000000e+00
14   SN - VTA -1.8661251 6.202386e-02 1.000000e+00
15  STR - VTA -3.5397799 4.004608e-04 8.409677e-03
16  DMV - XII  0.4602551 6.453331e-01 1.000000e+00
17   LC - XII -4.2008736 2.658870e-05 5.583627e-04
18    R - XII -3.6904089 2.238939e-04 4.701772e-03
19   SN - XII -3.9916667 6.561053e-05 1.377821e-03
20  STR - XII -5.6653216 1.467491e-08 3.081731e-07
21  VTA - XII -2.1255416 3.354145e-02 7.043703e-01

Estimation Statistics

dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  neuron
Y Variable :  mean_axon_per_var_px

Unpaired mean difference of VTA (n = 12) minus SN (n = 12)
 7.05 [95CI  3.24; 13.3]

Unpaired mean difference of LC (n = 12) minus SN (n = 12)
 0.197 [95CI  -3.3; 4.45]

Unpaired mean difference of R (n = 12) minus SN (n = 12)
 0.326 [95CI  -2.72; 2.68]

Unpaired mean difference of DMV (n = 12) minus SN (n = 12)
 45.6 [95CI  34.2; 72.2]

Unpaired mean difference of XII (n = 12) minus SN (n = 12)
 33.2 [95CI  24.8; 47.4]

Unpaired mean difference of STR (n = 12) minus SN (n = 12)
 -3.62 [95CI  -6.41; -1.89]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

PD-vulnerable vs PD-resilient


    Wilcoxon rank sum exact test

data:  mean_varicosity_lengthpervar_length$mean_axon_per_var_px by mean_varicosity_lengthpervar_length$type
W = 917, p-value = 0.6369
alternative hypothesis: true location shift is not equal to 0
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
The first five rows are:
# A tibble: 5 × 5
  neuron image mean_axon_per_var_px     n type         
  <fct>  <chr>                <dbl> <int> <fct>        
1 SN     SN_01                10.2    797 pd-vulnerable
2 SN     SN_02                 7.78   372 pd-vulnerable
3 SN     SN_03                 8.71   853 pd-vulnerable
4 SN     SN_04                 5.94   496 pd-vulnerable
5 SN     SN_05                 9.70   629 pd-vulnerable

X Variable :  type
Y Variable :  mean_axon_per_var_px

Effect sizes(s) will be computed for:
  1. pd-vulnerable minus non-vulnerable
dabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================

Good evening!
The current time is 19:30 pm on Wednesday March 09, 2022.

Dataset    :  .
X Variable :  type
Y Variable :  mean_axon_per_var_px

Unpaired mean difference of pd-vulnerable (n = 48) minus non-vulnerable (n = 36)
 -0.694 [95CI  -9.26; 9.77]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.